After reading this thread, the bold part is the biggest factor in play.
From a business stand point, people not wanting to participate in a area of your game should raise concern.
Why aren't they interested?
How do we keep them interested?
How do we make it more interesting for first timers?
These are the questions Bioware has to ask themselves in order for players to get involved in certain aspects of the game. One thing stands true, you are paying Bioware for a service. That service is in competition with a lot of other companies that will offer similar services. So the goal has to be making your service the better choice for entertainment purposes, after all it's a game.
Adding a deserter debuff just inconveniences a player. Any other paying services, something like this wouldn't fly with a customer. Go to a restaurant and order a steak rare, but it comes back well cooked. Chances are you will send it back and not have the waiter tell you "lol excuses".
Inconvenience a customer that is paying with their money? They'll take their business else where, simple as that.
Alot of good points here.